LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide

units		real
atom_style	full

pair_style	lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor	2.0 bin
neigh_modify	delay 5

timestep	2.0

thermo_style	multi
thermo		50

fix		1 all nvt temp 275.0 275.0 100.0 tchain 1
fix		2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles

group		peptide type <= 12
84 atoms in group peptide

#dump		1 peptide atom 10 dump.peptide

#dump		2 peptide image 25 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify	2 pad 3

#dump		3 peptide movie 25 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify	3 pad 3

#compute		bnd all property/local btype batom1 batom2
#dump		2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]

run		300
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
SHAKE stats (type/ave/delta) on step 0
  4 1.111 1.44264e-05
  6 0.996998 7.26967e-06
  8 1.08 1.32536e-05
  10 1.111 1.22749e-05
  12 1.08 1.11767e-05
  14 0.96 0
  18 0.957206 4.37979e-05
  31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =     -5237.4580 KinEng   =      1134.9186 Temp     =       282.1005 
PotEng   =     -6372.3766 E_bond   =        16.5572 E_angle  =        36.3726 
E_dihed  =        15.5190 E_impro  =         1.9426 E_vdwl   =       692.8945 
E_coul   =     26772.2646 E_long   =    -33907.9271 Press    =      -837.0112 
---------------- Step       50 ----- CPU =      1.0190 (sec) ----------------
TotEng   =     -5247.5537 KinEng   =      1132.4000 Temp     =       281.4745 
PotEng   =     -6379.9537 E_bond   =        12.2118 E_angle  =        31.7365 
E_dihed  =        18.8145 E_impro  =         2.3611 E_vdwl   =       658.1785 
E_coul   =     26804.4441 E_long   =    -33907.7003 Press    =     -1331.7946 
SHAKE stats (type/ave/delta) on step 100
  4 1.111 7.80613e-07
  6 0.997 1.06181e-06
  8 1.08 6.20292e-07
  10 1.111 6.23284e-07
  12 1.08 2.67996e-07
  14 0.96 0
  18 0.957201 5.3796e-06
  31 104.52 0.000502278
---------------- Step      100 ----- CPU =      2.0505 (sec) ----------------
TotEng   =     -5257.9979 KinEng   =      1078.0553 Temp     =       267.9663 
PotEng   =     -6336.0532 E_bond   =        14.4829 E_angle  =        43.4429 
E_dihed  =        15.2569 E_impro  =         2.3160 E_vdwl   =       708.3273 
E_coul   =     26786.6829 E_long   =    -33906.5621 Press    =      -648.6819 
---------------- Step      150 ----- CPU =      3.1208 (sec) ----------------
TotEng   =     -5287.2799 KinEng   =      1098.6028 Temp     =       273.0737 
PotEng   =     -6385.8827 E_bond   =        17.4925 E_angle  =        32.8594 
E_dihed  =        15.1624 E_impro  =         1.6522 E_vdwl   =       736.9675 
E_coul   =     26717.2655 E_long   =    -33907.2821 Press    =      -333.1829 
SHAKE stats (type/ave/delta) on step 200
  4 1.111 2.18698e-07
  6 0.997 1.50563e-07
  8 1.08 6.57499e-08
  10 1.111 5.54188e-07
  12 1.08 1.9884e-07
  14 0.96 0
  18 0.957201 3.59627e-06
  31 104.52 0.000388335
---------------- Step      200 ----- CPU =      4.1320 (sec) ----------------
TotEng   =     -5308.4468 KinEng   =      1100.4873 Temp     =       273.5421 
PotEng   =     -6408.9341 E_bond   =        18.2714 E_angle  =        33.3040 
E_dihed  =        16.8150 E_impro  =         2.6051 E_vdwl   =       686.3221 
E_coul   =     26736.1319 E_long   =    -33902.3837 Press    =     -1470.3401 
---------------- Step      250 ----- CPU =      5.2131 (sec) ----------------
TotEng   =     -5294.1568 KinEng   =      1071.0940 Temp     =       266.2360 
PotEng   =     -6365.2508 E_bond   =        14.2013 E_angle  =        39.1996 
E_dihed  =        19.4585 E_impro  =         3.1407 E_vdwl   =       753.4590 
E_coul   =     26714.0039 E_long   =    -33908.7139 Press    =      -189.6057 
SHAKE stats (type/ave/delta) on step 300
  4 1.111 3.79043e-06
  6 0.997001 3.6052e-06
  8 1.08 2.09369e-06
  10 1.111 5.6484e-06
  12 1.08 2.10676e-06
  14 0.96 0
  18 0.957202 7.72571e-06
  31 104.52 0.000806203
---------------- Step      300 ----- CPU =      6.2919 (sec) ----------------
TotEng   =     -5251.3662 KinEng   =      1123.7719 Temp     =       279.3299 
PotEng   =     -6375.1381 E_bond   =        14.2206 E_angle  =        38.4274 
E_dihed  =        18.1674 E_impro  =         2.3734 E_vdwl   =       715.3476 
E_coul   =     26745.4045 E_long   =    -33909.0791 Press    =      -471.5904 
Loop time of 6.29195 on 1 procs for 300 steps with 2004 atoms

Performance: 8.239 ns/day, 2.913 hours/ns, 47.680 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.8228     | 4.8228     | 4.8228     |   0.0 | 76.65
Bond    | 0.0094063  | 0.0094063  | 0.0094063  |   0.0 |  0.15
Kspace  | 0.523      | 0.523      | 0.523      |   0.0 |  8.31
Neigh   | 0.82602    | 0.82602    | 0.82602    |   0.0 | 13.13
Comm    | 0.03742    | 0.03742    | 0.03742    |   0.0 |  0.59
Output  | 0.00022697 | 0.00022697 | 0.00022697 |   0.0 |  0.00
Modify  | 0.068182   | 0.068182   | 0.068182   |   0.0 |  1.08
Other   |            | 0.00493    |            |       |  0.08

Nlocal:    2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11185 ave 11185 max 11185 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    708019 ave 708019 max 708019 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708019
Ave neighs/atom = 353.303
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

Total wall time: 0:00:06
